Bacteriophages (the viruses that infect bacteria) play key roles in microbial communities, but the functions of most of their genes remain unknown. Here, Boulay et al. present a machine-learning classifier that uses protein language models to assign functions to bacteriophage proteins more accurately than existing approaches.

Abstract. In complex ecosystems, the loss of certain species can trigger a cascade of secondary extinctions and invasions. However, our understanding of th

As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of th...

AbstractMotivation. Oxford Nanopore Technologies’ devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing c

Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.

Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

We are modern virus hunters, using metagenomic sequencing to discover viruses in a wide range of environments and hosts. Have fun exploring the marvels of microbiology on this website!

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...